I've got a number of trees bred up now, and this is some general observations (Note I'm using Forestry 2.0.0.9, what is in the FTB packs right now is 2.0.0.3. I had to upgrade for an alveary fix, but there are other fixes as well. The update in a few days will update to 2.0.0.10) I'm manually growing trees, and not using farms.
1) There appears to be no way other than forestry farms to farm fruit without breaking the leaves.
2) Manually breaking fruit leaves will spawn exactly one fruit every time it is ripe. Chopping down the wood and letting the leaf decay will spawn _several_ fruit per leaf block. Walnut trees can spawn nearly 2 stacks of walnuts if you let the leaves decay. Chestnut will spawn over 4 stacks. Both of my example trees are "default" stats and have not been bred to increased fruit.
3) The grafter will always, 100%, spawn a sapling for the first five times. It doesn't break until the sixth usage however, and the sixth usage will not spawn a sapling.
4) 2x2 trees require 4 saplings to bonemeal into growth. I presume 3x3 require 9
5) When a leaf mutates into a new breed, both "sides" of the sapling will be the new breed, and it will have all the new breed stats. Unlike bees, the only hybrids are saplings that _didn't_ mutate.
6) The visual indication that a leaf has mutated doesn't update on the client unless you get out of visual range. This means logging out, teleporting far away and back, walking away, or zoning to another dimension and back. This is more than a block-update issue, as placing a block next to the leaves won't work to update them - except if a leaf decays next to a mutated leaf, the mutated leaf will visually update when the other leaves decay.
7) Exactly identical saplings will not always stack - except if you shut the server down and reload they will start to stack. Unloading the chunk "might" work, but I work in a chunkloaded area. Simply logging out and back will not fix it.